Replacing impute2 with Beagle; Support for hg19 and hg38 reference genomes

[NagaComBio]

Replacing Impute2 with Beagle

• Changed the phasing routine. "Beagle" replaced the program "impute2". Files and tools were renamed accordingly.
• Renamed all tools and files from "imputeGenotype" to "phaseGenotype" (and so on) as the subroutine does not actually perform imputation but phasing.

Support for hg19 and hg38 reference genomes

• Hg38 reference genome GRCh38_decoy_ebv_phiX_alt_hla_chr.fa is supported now along with the older hg19.
• Liftover are done for homozygous deletion artefacts and no-control 1K window files for now. Once we have more samples analyzed with hg38, we will replace them.

Summary by CodeRabbit

• New Features
  • Major version update to 6.0.0 with significant changes including the replacement of the "impute2" program with "Beagle", renaming of tools and files, and addition of new mappability options.
  • Added support for the hg38 genome.
  • Introduced a new CNA type 'AMP'.
• Bug Fixes
  • Fixed minor bugs in version 5.1.0 and 5.0.1.
• Documentation
  • Updated instructions for downloading and processing reference genome files for GRCh38.
  • Updated method of phasing genotypes of SNP positions in the documentation.
• Refactor
  • Updated paths and added new variables related to Beagle imputation in the ACEseq configuration.
• Tests
  • Updated dependency version from COWorkflowsBasePlugin 1.2.1 to 1.4.2.
• Style
  • Updated shebang from #!/usr/bin/python to #!/usr/bin/env python in several scripts for better portability.
• Chores
  • Added the file "hg19_GRCh37_1000genomes" to the list of ignored patterns.